PDB Short entry for 1L1H HEADER DNA 16-FEB-02 1L1H TITLE CRYSTAL STRUCTURE OF THE QUADRUPLEX DNA-DRUG COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: OXYTRICHA FOUR-STRANDED DNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE SEQUENCE IS NATURALLY FOUND IN OXYTRICHA NOVA. KEYWDS G-QUADRUPLEX, OXYTRICHA, FOUR-STRANDED DNA, DNA EXPDTA X-RAY DIFFRACTION AUTHOR S.M.HAIDER,G.N.PARKINSON,S.NEIDLE REVDAT 3 16-AUG-23 1L1H 1 REMARK LINK REVDAT 2 24-FEB-09 1L1H 1 VERSN REVDAT 1 11-FEB-03 1L1H 0 JRNL AUTH S.M.HAIDER,G.N.PARKINSON,S.NEIDLE JRNL TITL STRUCTURE OF A G-QUADRUPLEX-LIGAND COMPLEX JRNL REF J.MOL.BIOL. V. 326 117 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12547195 JRNL DOI 10.1016/S0022-2836(02)01354-2 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : EVERY 10TH REFLECTION REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.229 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.144 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 651 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 6932 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 506 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 146 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1L1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1000015555. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-02 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : COPPER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6932 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.10900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 13.80 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1JPQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 27.72550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.36800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.72550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.36800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG A1001 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG A1003 C6 - N1 - C2 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG A1003 N3 - C4 - C5 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG A1004 O4' - C1' - N9 ANGL. DEV. = -6.0 DEGREES REMARK 500 DT A1005 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG A1010 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG A1010 C3' - O3' - P ANGL. DEV. = 10.0 DEGREES REMARK 500 DG B2001 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 DG B2003 O5' - C5' - C4' ANGL. DEV. = -5.1 DEGREES REMARK 500 DG B2003 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES REMARK 500 DT B2005 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DT B2007 C6 - N1 - C2 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT B2007 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 DG B2009 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B2010 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A6014 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A1001 O6 REMARK 620 2 DG A1002 O6 68.6 REMARK 620 3 DG A1011 O6 169.0 106.8 REMARK 620 4 DG A1012 O6 108.3 172.3 77.5 REMARK 620 5 K A6015 K 120.4 52.6 54.2 131.3 REMARK 620 6 DG B2003 O6 99.2 68.9 69.8 118.8 53.8 REMARK 620 7 DG B2004 O6 69.4 115.2 105.2 68.9 125.4 71.8 REMARK 620 8 DG B2009 O6 69.6 103.4 121.4 68.9 128.9 168.4 105.4 REMARK 620 9 DG B2010 O6 112.4 67.6 73.3 108.4 55.8 109.6 177.2 73.7 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B6013 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A1001 O6 REMARK 620 2 DG A1012 O6 101.6 REMARK 620 3 DG B2004 O6 65.2 67.1 REMARK 620 4 DT B2005 O2 94.5 127.9 76.0 REMARK 620 5 DT B2007 O2 78.0 154.7 131.8 77.0 REMARK 620 6 DG B2009 O6 66.3 68.1 102.3 158.6 89.3 REMARK 620 7 HOH B9006 O 162.1 69.2 96.9 80.6 117.0 120.6 REMARK 620 8 HOH B9218 O 140.7 98.5 154.0 99.2 69.6 91.1 57.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A6015 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A1002 O6 REMARK 620 2 DG A1003 O6 94.8 REMARK 620 3 DG A1010 O6 129.3 109.1 REMARK 620 4 DG A1011 O6 105.0 131.1 92.1 REMARK 620 5 K A6016 K 130.7 54.7 54.5 124.4 REMARK 620 6 DG B2002 O6 160.2 71.9 70.0 75.3 53.1 REMARK 620 7 DG B2003 O6 69.3 77.4 157.8 69.1 126.4 93.1 REMARK 620 8 DG B2010 O6 65.3 156.2 77.5 69.7 128.2 130.6 105.4 REMARK 620 9 DG B2011 O6 77.5 68.7 71.3 158.7 56.5 109.6 129.6 93.2 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A6016 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A1003 O6 REMARK 620 2 DG A1004 O6 70.3 REMARK 620 3 DG A1009 O6 167.7 120.5 REMARK 620 4 DG A1010 O6 100.6 169.2 69.3 REMARK 620 5 DG B2001 O6 101.7 72.1 77.8 116.4 REMARK 620 6 DG B2002 O6 67.8 113.9 100.9 65.9 69.3 REMARK 620 7 DG B2011 O6 63.2 104.7 115.9 65.3 164.2 99.2 REMARK 620 8 DG B2012 O6 115.1 77.0 74.9 102.8 119.2 168.6 73.9 REMARK 620 N 1 2 3 4 5 6 7 DBREF 1L1H A 1001 1012 PDB 1L1H 1L1H 1001 1012 DBREF 1L1H B 2001 2012 PDB 1L1H 1L1H 2001 2012 SEQRES 1 A 12 DG DG DG DG DT DT DT DT DG DG DG DG SEQRES 1 B 12 DG DG DG DG DT DT DT DT DG DG DG DG HET PYN A8001 34 HET K A6014 1 HET K A6015 1 HET K A6016 1 HET K B6013 1 HETNAM PYN 3-PYRROLIDIN-1-YL-N-[6-(3-PYRROLIDIN-1-YL- HETNAM 2 PYN PROPIONYLAMINO)-ACRIDIN-3-YL]-PROPIONAMIDE HETNAM K POTASSIUM ION FORMUL 3 PYN C27 H33 N5 O2 FORMUL 4 K 4(K 1+) FORMUL 8 HOH *146(H2 O) LINK O6 DG A1001 K K A6014 1555 1555 2.79 LINK O6 DG A1001 K K B6013 1555 1555 3.01 LINK O6 DG A1002 K K A6014 1555 1555 2.77 LINK O6 DG A1002 K K A6015 1555 1555 2.76 LINK O6 DG A1003 K K A6015 1555 1555 2.81 LINK O6 DG A1003 K K A6016 1555 1555 2.97 LINK O6 DG A1004 K K A6016 1555 1555 2.72 LINK O6 DG A1009 K K A6016 1555 1555 2.63 LINK O6 DG A1010 K K A6015 1555 1555 2.78 LINK O6 DG A1010 K K A6016 1555 1555 2.95 LINK O6 DG A1011 K K A6014 1555 1555 2.76 LINK O6 DG A1011 K K A6015 1555 1555 2.83 LINK O6 DG A1012 K K A6014 1555 1555 2.77 LINK O6 DG A1012 K K B6013 1555 1555 2.80 LINK K K A6014 K K A6015 1555 1555 3.35 LINK K K A6014 O6 DG B2003 1555 1555 2.87 LINK K K A6014 O6 DG B2004 1555 1555 2.75 LINK K K A6014 O6 DG B2009 1555 1555 2.81 LINK K K A6014 O6 DG B2010 1555 1555 2.72 LINK K K A6014 K K B6013 1555 1555 3.46 LINK K K A6015 K K A6016 1555 1555 3.51 LINK K K A6015 O6 DG B2002 1555 1555 2.74 LINK K K A6015 O6 DG B2003 1555 1555 2.85 LINK K K A6015 O6 DG B2010 1555 1555 2.89 LINK K K A6015 O6 DG B2011 1555 1555 2.77 LINK K K A6016 O6 DG B2001 1555 1555 2.74 LINK K K A6016 O6 DG B2002 1555 1555 2.88 LINK K K A6016 O6 DG B2011 1555 1555 3.04 LINK K K A6016 O6 DG B2012 1555 1555 2.65 LINK O6 DG B2004 K K B6013 1555 1555 2.84 LINK O2 DT B2005 K K B6013 1555 1555 2.80 LINK O2 DT B2007 K K B6013 1555 1555 2.55 LINK O6 DG B2009 K K B6013 1555 1555 2.83 LINK K K B6013 O HOH B9006 1555 1555 3.05 LINK K K B6013 O HOH B9218 1555 1555 2.67 SITE 1 AC1 8 DT A1006 DT A1007 DT A1008 DG A1009 SITE 2 AC1 8 DG B2001 DT B2008 DG B2012 HOH B9003 SITE 1 AC2 9 DG A1001 DG A1012 K A6014 DG B2004 SITE 2 AC2 9 DT B2005 DT B2007 DG B2009 HOH B9006 SITE 3 AC2 9 HOH B9218 SITE 1 AC3 10 DG A1001 DG A1002 DG A1011 DG A1012 SITE 2 AC3 10 K A6015 DG B2003 DG B2004 DG B2009 SITE 3 AC3 10 DG B2010 K B6013 SITE 1 AC4 10 DG A1002 DG A1003 DG A1010 DG A1011 SITE 2 AC4 10 K A6014 K A6016 DG B2002 DG B2003 SITE 3 AC4 10 DG B2010 DG B2011 SITE 1 AC5 9 DG A1003 DG A1004 DG A1009 DG A1010 SITE 2 AC5 9 K A6015 DG B2001 DG B2002 DG B2011 SITE 3 AC5 9 DG B2012 CRYST1 55.451 42.736 26.926 90.00 90.00 90.00 P 21 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018034 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023399 0.000000 0.00000 SCALE3 0.000000 0.000000 0.037139 0.00000